DNA base stacking involving adenine and 2-aminopurine

The potential energy surfaces of stacked structures consisting of adenine (A) and 2-aminopurine (2AP) have been investigated in the gas phase. Both face-to-back (the double ring system of one base exactly on top of that of the other one) and face-to-face (one base flipped by 180°) A/A, 2AP/2AP and A/2AP stacks were considered. Minima and transition states were optimised at the counterpoise-corrected M06-2X/6-31+G(d) level of theory. For each type of stack, between five and nine minima were located, usually connected by low barriers of 1-2 kcal/mol. This shows the large conformational flexibility of these stacked base pairs. The double-ring system in A and 2AP affords multiple minima with similar twist angles, making the potential energy surface of stacks comprising of purine bases more complex than those of pyrimidine stacks. The locations of the stationary points on the potential energy surface differ for the three different systems; thus, the replacement of A by 2AP in a base stack changes its potential energy landscape.Publisher PDFPeer reviewe

Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: water systems

The competition between hydrogen- and halogen-bonding interactions in complexes of 5-halogenated 1-methyluracil (XmU; X = F, Cl, Br, I or At) with one or two water molecules in the binding region between C5-X and C4=O4 is investigated with M06-2X/6-31+G(d). In the singly-hydrated systems, the water molecule forms a hydrogen bond with C4=O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5-X exist only for X = Br, I and At. Structures with two waters forming a bridge between C4=O and C5-X (through hydrogen- and halogen-bonding interactions) exist for all halogens except F. The absence of a halogen-bonded structure in singly-hydrated ClmU is therefore attributed to the competing hydrogen-bonding interaction with C4=O4. The halogen-bond angle in the doubly-hydrated structures (150-160°) is far from the expected linearity of halogen bonds, indicating that significantly non-linear halogen bonds may exist in complex environments with competing interactions.PostprintPeer reviewe

Corrigendum : Competition between hydrogen and halogen bonding in halogenated 1-methyluracil:water systems

This article corrects: Competition between hydrogen and halogen bonding in halogenated 1-methyluracil:water systems, Volume 37, Issue 8, 763-770. Article first published online: 15 January 2016.PostprintPeer reviewe

Plant Performance in Precision Horticulture: Optimal climate control under stochastic uncertainty

This paper presents a risk mitigating, time-varying feedback control algorithm for crop production when state dynamics are subject to uncertainty. The model based case study concerns a 40 day production round of lettuce in a greenhouse where control input consists of daily and nightly temperature set points. The control problem was formulated in terms of a stochastic Markov decision process with the objective to maximize the expected net revenue at harvest time. The importance of time-varying feedback and of risk mitigation was investigated by making a comparison with a controller that takes uncertainty into account but is static and a controller which is dynamic but ignores the uncertainty in the state dynamics. For the case of heat limited crop growth, and strict requirements on harvest weight precision, the dynamic stochastic controller outperformed the static controller in terms of both maximal expected net revenue (by 19 %) and state precision at harvest time (with 50 % less standard deviation). It also outperformed the deterministic controller for both criteria (15 % in maximal expected net revenue and 8 % less standard deviation). A detailed sensitivity analysis showed that such improvements in performance levels are robust, since they hold over large ranges of uncertainty in state dynamics, required harvest precision levels, starting days, and initial weights. The results provide insights in potential of dynamic feedback and risk mitigation strategies for high precision requirements under uncertainty. Although the results should be interpreted with caution, they illustrate the considerable potential benefit for stochastic greenhouse climate control under uncertainty when high precision is required

Simulation of organ patterning on the floral meristem using a polar auxin transport model

An intriguing phenomenon in plant development is the timing and positioning of lateral organ initiation, which is a fundamental aspect of plant architecture. Although important progress has been made in elucidating the role of auxin transport in the vegetative shoot to explain the phyllotaxis of leaf formation in a spiral fashion, a model that explains the whorled organ patterning in the expanding floral meristem is not available yet. We present an initial simulation approach to study the mechanisms that are expected to play an important role. Starting point is a confocal imaging study of Arabidopsis floral meristems at consecutive time points during flower development. These images reveal auxin accumulation patterns at the positions of the organs, which strongly suggests that the role of auxin in the floral meristem is similar to the role it plays in the shoot apical meristem. This is the basis for a simulation study of auxin transport through a growing floral meristem, which may answer the question whether auxin transport can in itself be responsible for the typical whorled floral pattern. We combined a cellular growth model for the meristem with a polar auxin transport model. The model predicts that sepals are initiated by auxin maxima arising early during meristem outgrowth. These form a pre-pattern relative to which a series of smaller auxin maxima are positioned, which partially overlap with the anlagen of petals, stamens, and carpels. We adjusted the model parameters corresponding to properties of floral mutants and found that the model predictions agree with the observed mutant patterns. The predicted timing of the primordia outgrowth and the timing and positioning of the sepal primordia show remarkable similarities with a developing flower in nature

Social system of transition society theoretical scheme: economy, culture and ecology interrelations

Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a diseased state. The method employs a mathematical model, for which the kinetics of gene regulation, splicing, elongation and mRNA degradation were estimated from experimental data of transcriptional dynamics. The time-dependent dynamics of several species of adipose differentiation-related protein (ADRP) mRNA were measured in response to ligand activation of the transcription factor peroxisome proliferator-activated receptor δ (PPARδ). We validated the method by monitoring the mRNA dynamics upon gene activation in the presence of a splicing inhibitor. Our mathematical model correctly identifies splicing as the inhibitor target, despite the noise in the data

Effect of nickel and cobalt on methanogenic enrichment cultures and role of biogenic sulfide in metal toxicity attenuation

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2017.01341/full#supplementary-materialMetals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulphide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulphate or sulphide. The addition of sulphide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulphate, possibly due to competition of hydrogenotrophic methanogens by sulphate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulphide had a positive effect and more methane was produced in these incubations than in similar assays without sulphate addition. The outcome of competition between methanogens and sulphate-reducing bacteria is a determinant factor for the success of using biogenic sulphide as detoxification method.The research was financially supported by the People Program (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013 under REA agreement 289193. Research of AS and DS is supported by a ERC grant (project 323009) of the European Union Seventh Framework Program FP7 and a Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO).info:eu-repo/semantics/publishedVersio

Bicuspid Aortic Valve Stenosis and the Effect of Vitamin K2 on Calcification Using F-Sodium Fluoride Positron Emission Tomography/Magnetic Resonance:The BASIK2 Rationale and Trial Design

BASIK2 is a prospective, double-blind, randomized placebo-controlled trial investigating the effect of vitamin K2 (menaquinone-7;MK7) on imaging measurements of calcification in the bicuspid aortic valve (BAV) and calcific aortic valve stenosis (CAVS). BAV is associated with early development of CAVS. Pathophysiologic mechanisms are incompletely defined, and the only treatment available is valve replacement upon progression to severe symptomatic stenosis. Matrix Gla protein (MGP) inactivity is suggested to be involved in progression. Being a vitamin K dependent protein, supplementation with MK7 is a pharmacological option for activating MGP and intervening in the progression of CAVS. Forty-four subjects with BAV and mild–moderate CAVS will be included in the study, and baseline 18F-sodiumfluoride (18F-NaF) positron emission tomography (PET)/ magnetic resonance (MR) and computed tomography (CT) assessments will be performed. Thereafter, subjects will be randomized (1:1) to MK7 (360 mcg/day) or placebo. During an 18-month follow-up period, subjects will visit the hospital every 6 months, undergoing a second 18F-NaF PET/MR after 6 months and CT after 6 and 18 months. The primary endpoint is the change in PET/MR 18F-NaF uptake (6 months minus baseline) compared to this delta change in the placebo arm. The main secondary endpoints are changes in calcium score (CT), progression of the left ventricularremodeling response and CAVS severity (echocardiography). We will also examine the association between early calcification activity (PET) and later changes in calcium score (CT)